Tue Nov 22 14:16:22 PST 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Nov 22 2011 at 14:16:23 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1989 !!! WARNING: GLM 197 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6038606 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -24.48600 34.46800 ymin,ymax (A): -17.91600 20.00600 zmin,zma (A): -3.754000 38.29800 x,y,z range (A): 58.95400 37.92200 42.05200 scale (grids/A): 0.6038606 object centre (A): 4.991001 1.045000 17.27200 number of atom coordinates read : 1989 total number of charged atoms : 1853 net assigned charge : 1.906005 assigned positive charge : 294.4260 centred at (gu) : 90.10081 90.04622 90.28161 assigned negative charge : -292.5203 centred at (gu) : 90.13163 90.11634 90.41612 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4904 nv = 96 ne = 84 npr = 39594 no. pairs analyzed = 39594 no. exposed pairs = 2652 no. arc points = 18121 no. surface atoms = 907 nbur = 1082 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 251 mr = 2555 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1848 ## 193 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 5954 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7372821E-09 -3.5131396E-09 midg,1,midg; midg,igrid,midg 3.0687495E-09 -1.2597305E-09 1,midg,midg; igrid,midg,midg 1.8546803E-09 -1.5026686E-11 gauss-seidel spectral radius is 0.9857562 estimated iterations to convergence 69 setup time was (sec) 0.4500000 now iterating at: 14:16:24 rms-change max change #iterations 0.1006210 20.06050 at 10iterations 8.4642256E-03 1.449127 at 20iterations 7.3147472E-04 0.1437674 at 30iterations 6.2616396E-05 1.0077477E-02 at 40iterations 5.4789443E-06 9.5176697E-04 at 50iterations finished qdiffx linear iterations at : 14:16:30 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 5.4789443E-06 9.5176697E-04 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 14:16:31 3.198u 0.158s 0:07.68 43.4% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Nov 22 2011 at 14:16:33 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1989 !!! WARNING: GLM 197 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.811582 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -24.48600 34.46800 ymin,ymax (A): -17.91600 20.00600 zmin,zma (A): -3.754000 38.29800 x,y,z range (A): 58.95400 37.92200 42.05200 scale (grids/A): 1.811582 object centre (A): 4.991001 1.045000 17.27200 number of atom coordinates read : 1989 total number of charged atoms : 1853 net assigned charge : 1.906005 assigned positive charge : 294.4260 centred at (gu) : 90.30255 90.13869 90.84471 assigned negative charge : -292.5203 centred at (gu) : 90.39511 90.34918 91.24860 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 52415 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18121 grid for indexing accessible points = 1.400000 m= 18989 mr = 35088 m= 2738 mr = 13820 m= 124 mr = 1599 m= 3 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 23728 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 14470 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6038606 object centre at (A) : 4.991001 1.045000 17.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7936806E-03 -8.1410035E-03 midg,1,midg; midg,igrid,midg 9.4372337E-04 -3.1722656E-03 1,midg,midg; igrid,midg,midg 4.2435493E-02 2.9627325E-02 gauss-seidel spectral radius is 0.9984252 estimated iterations to convergence 200 setup time was (sec) 0.6400000 now iterating at: 14:16:37 rms-change max change #iterations 3.290298 149.4205 at 10iterations 1.448327 55.27758 at 20iterations 0.6423082 27.24602 at 30iterations 0.2831703 11.73876 at 40iterations 0.1247457 5.560112 at 50iterations 5.5071879E-02 2.139824 at 60iterations 2.4452571E-02 0.9178195 at 70iterations 1.0793653E-02 0.4250890 at 80iterations 4.7970759E-03 0.1839422 at 90iterations 2.1138371E-03 8.2546234E-02 at 100iterations 9.3773927E-04 3.5820007E-02 at 110iterations 4.1596254E-04 1.5533447E-02 at 120iterations finished qdiffx linear iterations at : 14:16:55 total time elapsed so far: 6.470000 # loops : 120 mean,max change (kT/e) : 4.1596254E-04 1.5533447E-02 energy calculations done at 6.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.640000 DelPhi exited at 14:16:56 6.644u 0.144s 0:23.80 28.4% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Nov 22 2011 at 14:17:02 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1989 !!! WARNING: GLM 197 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.717373 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -24.48600 34.46800 ymin,ymax (A): -17.91600 20.00600 zmin,zma (A): -3.754000 38.29800 x,y,z range (A): 58.95400 37.92200 42.05200 scale (grids/A): 2.717373 object centre (A): 4.991001 1.045000 17.27200 number of atom coordinates read : 1989 total number of charged atoms : 1853 net assigned charge : 1.906005 assigned positive charge : 294.4260 centred at (gu) : 90.45383 90.20802 91.26707 assigned negative charge : -292.5203 centred at (gu) : 90.59279 90.52379 91.87295 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 120927 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18121 grid for indexing accessible points = 1.400000 m= 60758 mr = 85041 m= 21920 mr = 49133 m= 4854 mr = 17439 m= 550 mr = 3547 m= 28 mr = 337 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 53539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 14818 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.811582 object centre at (A) : 4.991001 1.045000 17.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8195747E-02 -7.3194332E-02 midg,1,midg; midg,igrid,midg -1.8919801E-02 -2.9845743E-02 1,midg,midg; igrid,midg,midg 0.4694748 0.3526413 gauss-seidel spectral radius is 0.9991870 estimated iterations to convergence 277 setup time was (sec) 1.240000 now iterating at: 14:17:08 rms-change max change #iterations 8.104114 343.5215 at 10iterations 4.682113 137.7111 at 20iterations 2.662536 67.33427 at 30iterations 1.516574 37.53574 at 40iterations 0.8542380 19.82404 at 50iterations 0.4814804 11.30391 at 60iterations 0.2714639 6.385584 at 70iterations 0.1523741 3.587677 at 80iterations 8.5507274E-02 1.938498 at 90iterations 4.8173726E-02 1.124367 at 100iterations 2.6983719E-02 0.6299839 at 110iterations 1.5092722E-02 0.3559875 at 120iterations 8.4506087E-03 0.1953878 at 130iterations 4.7300458E-03 9.6585274E-02 at 140iterations 2.6551068E-03 5.6800842E-02 at 150iterations 1.4860579E-03 3.2006264E-02 at 160iterations 8.2880340E-04 2.0564139E-02 at 170iterations 4.6296298E-04 1.0169983E-02 at 180iterations finished qdiffx linear iterations at : 14:17:38 total time elapsed so far: 11.03000 # loops : 180 mean,max change (kT/e) : 4.6296298E-04 1.0169983E-02 energy calculations done at 11.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.21000 DelPhi exited at 14:17:39 11.212u 0.199s 0:38.30 29.7% 0+0k 0+0io 0pf+0w